- Introduction to single-cell RNA-seq
- Quality control and normalization
- Survey of downstream analysis methodology
July 6, 2019
image source: http://carbonandsilicon.net/rblogging/2018/02/27/UMAP_plots
Andrews & Hemburg 2018 (https://doi.org/10.1016/j.mam.2017.07.002)
Risso et al 2018 (https://doi.org/10.1371/journal.pcbi.1006378)
Korthauer et al 2016 (https://doi.org/10.1186/s13059-016-1077-y)
Korthauer et al 2016 (https://doi.org/10.1186/s13059-016-1077-y)
Soneson & Robinson 2018 (https://doi.org/10.1038/nmeth.4612)
library(TENxBrainData) assay(TENxBrainData(), "counts", withDimnames = FALSE)
## <27998 x 1306127> HDF5Matrix object of type "integer": ## [,1] [,2] [,3] [,4] ... [,1306124] ## [1,] 0 0 0 0 . 0 ## [2,] 0 0 0 0 . 0 ## [3,] 0 0 0 0 . 0 ## [4,] 0 0 0 0 . 0 ## [5,] 0 0 0 0 . 0 ## ... . . . . . . ## [27994,] 0 0 0 0 . 0 ## [27995,] 1 0 0 2 . 0 ## [27996,] 0 0 0 0 . 0 ## [27997,] 0 0 0 0 . 0 ## [27998,] 0 0 0 0 . 0 ## [,1306125] [,1306126] [,1306127] ## [1,] 0 0 0 ## [2,] 0 0 0 ## [3,] 0 0 0 ## [4,] 0 0 0 ## [5,] 0 0 0 ## ... . . . ## [27994,] 0 0 0 ## [27995,] 1 0 0 ## [27996,] 0 0 0 ## [27997,] 0 0 0 ## [27998,] 0 0 0
For a gentle introduction to the nitty gritty details of how the DelayedArray framework works, see the tutorial “Effectively using the DelayedArray framework for users” from the 2019 Bioconductor meeting
For practice using scater and scran with HDF5 files the tutorial “Analysis of Large Single-Cell RNA-Seq Datasets in R/Bioconductor”, also from the 2019 Bioconductor meeting
Zappia, Phipson & Oshlack 2018 (https://doi.org/10.1371/journal.pcbi.1006245)
BiocManager::install("scDD")
BiocManager::install("MAST")